NM_001364171.2:c.1404+8A>G

Variant names:

• chr19-48298169-T-C
• rs8111947
• NM_001364171.2:c.1404+8A>G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001364171.2(ODAD1):​c.1404+8A>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 1,610,912 control chromosomes in the GnomAD database, including 104,786 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.37 (10563 hom., cov: 30)
  • Exomes 𝑓: 0.35 (94223 hom.)
• Consequence: ODAD1 NM_001364171.2 splice_region, intron
• Scores: Splicing: ADA: 0.00001091
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:5
• Conservation: PhyloP100: -2.32

Genes affected

ODAD1 (HGNC:26560): (outer dynein arm docking complex subunit 1) This gene encodes a coiled-coil domain-containing protein that is a component of the outer dynein arm docking complex in cilia cells. Mutations in this gene may cause primary ciliary dyskinesia 20. [provided by RefSeq, May 2013]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BP6: Variant 19-48298169-T-C is Benign according to our data. Variant chr19-48298169-T-C is described in ClinVar as [Benign]. Clinvar id is 262486.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ODAD1	NM_001364171.2	c.1404+8A>G		splice_region_variant, intron_variant	Intron 13 of 15	ENST00000674294.1	NP_001351100.1
ODAD1	NM_144577.4	c.1293+8A>G		splice_region_variant, intron_variant	Intron 11 of 13		NP_653178.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ODAD1	ENST00000674294.1	c.1404+8A>G		splice_region_variant, intron_variant	Intron 13 of 15		NM_001364171.2	ENSP00000501363.1

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55257 AN: 150932 Hom.: 10542 Cov.: 30

Gnomad AFR AF: 0.443

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.364

GnomAD3 exomes AF: 0.318 AC: 79524 AN: 249742 Hom.: 13757 AF XY: 0.324 AC XY: 43765 AN XY: 135146

Gnomad AFR exome AF: 0.437

Gnomad AMR exome AF: 0.175

Gnomad ASJ exome AF: 0.442

Gnomad EAS exome AF: 0.127

Gnomad SAS exome AF: 0.294

Gnomad FIN exome AF: 0.333

Gnomad NFE exome AF: 0.368

Gnomad OTH exome AF: 0.333

GnomAD4 exome AF: 0.353 AC: 515679 AN: 1459860 Hom.: 94223 Cov.: 42 AF XY: 0.352 AC XY: 255473 AN XY: 726314

Gnomad4 AFR exome AF: 0.448

Gnomad4 AMR exome AF: 0.186

Gnomad4 ASJ exome AF: 0.443

Gnomad4 EAS exome AF: 0.115

Gnomad4 SAS exome AF: 0.290

Gnomad4 FIN exome AF: 0.330

Gnomad4 NFE exome AF: 0.369

Gnomad4 OTH exome AF: 0.351

GnomAD4 genome AF: 0.366 AC: 55313 AN: 151052 Hom.: 10563 Cov.: 30 AF XY: 0.360 AC XY: 26564 AN XY: 73724

Gnomad4 AFR AF: 0.443

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.441

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.276

Gnomad4 FIN AF: 0.337

Gnomad4 NFE AF: 0.369

Gnomad4 OTH AF: 0.363

Alfa AF: 0.373 Hom.: 4598

Bravo AF: 0.362

Asia WGS AF: 0.212 AC: 743 AN: 3478

EpiCase AF: 0.375

EpiControl AF: 0.369

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:2

Mar 29, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

-

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided Benign:2

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Nov 10, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Primary ciliary dyskinesia Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.64
DANN	Benign	0.49

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.000011
dbscSNV1_RF	Benign	0.0040
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs8111947; hg19: chr19-48801426; COSMIC: COSV59558635;